I too went into my email account and checked the Notes folder only to see that what I was looking for was also deleted from this place. But, if like me, you have your account to setup to Archive instead of actually delete, they're still in there. So I went to the Email Search Bar at the top, typed in a word from the Note for which I was looking, hit Search/Enter and there in that list of results I found the missing Note. It took me minute to figure out how to get it back into my Notes folder. The simplicity of it stumped me for a moment;
Open the document, then simply click on the Label tab (has picture of tag on it) at the top, and select the Notes label. The document in question will immediately be moved to your Notes folder on both your computer and your phone.
I hope this was helpful.